SMTL ID : 6td5.1

Leishmania tarentolae proteasome 20S subunit complexed with LXE408 and bortezomib

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-2-2-2-2-2-2-2-2-2-2-mer

Ligands

6 x BO2: N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE(Covalent)

BO2.1: 13 residues within 4Å: Chain H: T.1, R.19, T.20, S.21, S.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52 Chain I: S.118 11 PLIP interactions: 10 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:T.20, H:K.33, H:R.45 Hydrogen bonds: H:T.1, H:S.21, H:S.21, H:G.47, H:G.47, H:G.47, H:A.49, I:S.118 BO2.2: 12 residues within 4Å: Chain I: T.1, D.17, R.19, A.20, T.21, E.22, K.33, A.46, G.47, T.48, S.49, Y.168 8 PLIP interactions: 8 interactions with chain I Hydrophobic interactions: I:T.1, I:A.20 Hydrogen bonds: I:T.1, I:T.21, I:T.21, I:G.47, I:S.49, I:S.49 BO2.3: 15 residues within 4Å: Chain L: T.1, R.19, A.20, S.21, T.22, A.27, V.31, K.33, L.45, G.47, G.48, A.49, A.169 Chain M: S.255 Ligands: N2E.4 11 PLIP interactions: 10 interactions with chain L, 1 interactions with chain M Hydrophobic interactions: L:V.31, L:L.45, L:A.49 Hydrogen bonds: L:T.1, L:S.21, L:S.21, L:K.33, L:G.47, L:G.47, L:A.49, M:S.255 BO2.5: 13 residues within 4Å: Chain V: T.1, R.19, T.20, S.21, S.22, K.33, R.45, S.46, G.47, S.48, A.49, T.52 Chain W: S.118 11 PLIP interactions: 10 interactions with chain V, 1 interactions with chain W Hydrophobic interactions: V:T.20, V:K.33, V:R.45 Hydrogen bonds: V:T.1, V:S.21, V:S.21, V:G.47, V:G.47, V:G.47, V:A.49, W:S.118 BO2.6: 12 residues within 4Å: Chain W: T.1, D.17, R.19, A.20, T.21, E.22, K.33, A.46, G.47, T.48, S.49, Y.168 8 PLIP interactions: 8 interactions with chain W Hydrophobic interactions: W:T.1, W:A.20 Hydrogen bonds: W:T.1, W:T.21, W:T.21, W:G.47, W:S.49, W:S.49 BO2.7: 16 residues within 4Å: Chain 0: D.251, S.255 Chain Z: T.1, R.19, A.20, S.21, T.22, A.27, V.31, K.33, L.45, G.47, G.48, A.49, A.169 Ligands: N2E.8 11 PLIP interactions: 11 interactions with chain Z Hydrophobic interactions: Z:A.20, Z:V.31, Z:L.45, Z:A.49 Hydrogen bonds: Z:T.1, Z:S.21, Z:S.21, Z:G.47, Z:G.47, Z:G.47, Z:A.49

2 x N2E: ~{N}-[4-fluoranyl-3-[6-(3-methylpyridin-2-yl)-[1,2,4]triazolo[1,5-a]pyrimidin-2-yl]phenyl]-2,4-dimethyl-1,3-oxazole-5-carboxamide(Non-covalent)

N2E.4: 18 residues within 4Å: Chain K: F.24, I.29 Chain L: T.1, S.21, A.46, G.47, S.96, G.98, Y.113, F.126, S.127, V.128, G.129, S.130, S.132, Y.136, A.169 Ligands: BO2.3 14 PLIP interactions: 10 interactions with chain L, 4 interactions with chain K Hydrophobic interactions: L:Y.113, L:F.126, L:Y.136, K:F.24, K:F.24, K:I.29 Hydrogen bonds: L:G.47, L:Y.113, L:Y.113, L:G.129, L:S.130, L:S.132 Halogen bonds: L:S.96 pi-Stacking: K:F.24 N2E.8: 18 residues within 4Å: Chain Y: F.24, I.29 Chain Z: T.1, S.21, G.23, G.47, S.96, M.97, G.98, Y.113, S.127, V.128, G.129, S.130, S.132, Y.136, A.169 Ligands: BO2.7 10 PLIP interactions: 7 interactions with chain Z, 3 interactions with chain Y Hydrophobic interactions: Z:Y.113, Z:V.128, Y:F.24, Y:I.29 Hydrogen bonds: Z:G.47, Z:Y.113, Z:G.129, Z:S.130 Halogen bonds: Z:S.96 pi-Stacking: Y:F.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nagle, A. et al., Discovery and Characterization of Clinical Candidate LXE408 as a Kinetoplastid-Selective Proteasome Inhibitor for the Treatment of Leishmaniases. J.Med.Chem. (2020)

Release Date

2020-08-26

Peptides

Proteasome subunit alpha type: AO
Proteasome subunit alpha type: BP
Proteasome subunit alpha type: CQ
Proteasome endopeptidase complex: DR
Proteasome subunit alpha type: ES
Proteasome subunit alpha type: FT
Proteasome endopeptidase complex: GU
Proteasome subunit beta: HV
Proteasome subunit beta: IW
Proteasome subunit beta: JX
Proteasome subunit family protein: KY
Proteasome subunit beta: LZ
Proteasome subunit beta: M0
Proteasome subunit beta: N1

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

O
a

B
B

P
b

C
C

Q
c

D
D

R
d

E
E

S
e

F
F

T
f

G
G

U
g

H
H

V
h

I
I

W
i

J
J

X
j

K
K

Y
k

L
L

Z
l

M
M

0
m

N
N

1
n

Proteasome subunit alpha type

Proteasome subunit alpha type

Proteasome subunit alpha type

Proteasome endopeptidase complex

Proteasome subunit alpha type

Proteasome subunit alpha type

Proteasome endopeptidase complex

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit family protein

Proteasome subunit beta

Proteasome subunit beta

Proteasome subunit beta

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